Skip to content

input_grrm_advvv

esta.grrmBag.input_grrm_advvv

GenerateCom

python class to generate input files (*.com file) for different type of calculations for GRRM using:
- non-supported - orca - gaussian

Notes

Different types of calculation are carried out by the

GRRM software given below:

    calculaiton type                          .... status of Implementation

=============================================================================== 1) - Normal mode analysis (FREQ) - Minimum point optimization (MIN) ......DONE - Saddle-point optimization (SADDLE) - IRC following (IRC) - LUP path optimization (LUP) .... DONE

-- to do 
Crossing point (MECI or MESX) optimization ....  will not be done
Crossing point (MECI or MESX) estimation   ....  will not be done
External atoms (microiterations)
Frozen atoms                               .... DONE

2)

MIN-AFIR calculations                      ...  DONE
AFIR calculations                          ...  DONE
DS-AFIR calculations                       ...  DONE

Refinement calculations                    ..... TODO

author: skumar email: sonukumar.physics@gmail.com

read_xyz()

Parameters

filename : str xyz file name

Returns

atomic positions : array rank 2 array of shape (natoms, 3) atomic labels : list/array of strings rank 1 array of atomic labels strings : string string mentioning the units of coordinates

read_xyz2(xyz2file)

Returns:

  • atomic positions: array: rank 2 array of shape (natoms, 3) –

    atomic labels: list/array of strings: rank 1 array of atomic labels no of atoms: scalar

flags_grrm(**kwargs)

options in GRRM code for calculation types

.. note::
Options sublink=/home/kumarsonu/bin/link_excode_allv3.1_.py Add Interaction Fragm.1=56,57,58,1 Fragm.2=59-62 1 2 Gamma=200.0 END NOFC KeepIntFiles DownDC=12

write_com(interface=None, basis=None, solvent=None, log_filename=None, Frozen_dict=None, lflags_file=False, gamma=None, **kwargs)

Parameters:

  • interface –

    name of the interface name

  • please –
  • atomic –
  • atomic –
  • no –
  • kwargs –

Returns:

  • input com GRRM file containing info of atomic structure as well –

    as other GRRM parameteres

write_com_2xyz(xyz2file, interface=None, **kwargs)

xyz files of products read from command line arguments ....mainly used for creating DS-AFIR input file ...

Returns:

  • com file containing info of atomic structure info of two atomic systems –

write_inp(xyzfile, charge, multiplicity, ncores=None, memory=None, log_filename=None, interface=None, gamma=None, **kwargs0)

generate input file for ORCA like below:

Parameters:

  • prefix –

    name of inp file with .inp extension

  • charge –

    chare on ths system

  • multiplicity –

    spin multiplicity (2S+1); for a single electron: S =½

Returns:

  • file ( string ) –

    inp file for orca containg charge and multiplicity options

Notes 
! XTB2 NoUseSym @job

* xyz  0 1
@geometry
*

write_input_oniom()

get input file for the oniom-msm method by suzuki etal. (ICReDD) for: - saddle calculations (see general folder for the implementation) - EQ/TS sampling calculations (this may not be possible as I tried setting up the calculation, but failed!!)

  • ReStruct calculation ..

freeze_notfreeze_atoms(fix_atm_list=None)

Parameters:

  • xyzfile (name of the xyz file containing xyz coords, and symbols) –
  • fix_atm_list –

Returns:

  • frozen_tuple ( tuple ) –

    tuple containg fixed atomic_positins, atomic_symbols, and atom index

  • not_frozen_tuple ( tuple ) –

    tuple containg not fixed atomic_positins, atomic_symbols, and atom index

freeze_notfreeze_atoms_(fix_atm_list=None)

Parameters:

  • xyzfile (name of the xyz file containing xyz coords, and symbols) –
  • fix_atm_list –

    all atom ranging from i-m are taken including the last index m.

Returns:

  • frozen_tuple ( tuple ) –

    tuple containg fixed atomic_positins, atomic_symbols, and atom index

  • not_frozen_tuple ( tuple ) –

    tuple containg not fixed atomic_positins, atomic_symbols, and atom index